Discovery of the structure of DNA

The structure of DNA double helix and how it was discovered. Chargaff, Watson and Crick, and Wilkins and Franklin.

Introduction

Today, the DNA double helix is probably the most iconic of all biological molecules. It's inspired staircases, decorations, pedestrian bridges (like the one in Singapore, shown below), and more.

I have to agree with the architects and designers: the double helix is a beautiful structure, one whose form fits its function in a remarkable way. But the double helix was not always part of our cultural lexicon. In fact, until the 1950s, the structure of DNA remained a mystery.

In this article, we'll briefly explore how the double-helical structure of DNA was discovered through the work of James Watson, Francis Crick, Rosalind Franklin, and other researchers. Then, we'll take a look at the properties of the double helix itself.

The components of DNA

From the work of biochemist Phoebus Levene and others, scientists in Watson and Crick's time knew that DNA was composed of subunits called nucleotides1^11. A nucleotide is made up of a sugar (deoxyribose), a phosphate group, and one of four nitrogenous bases: adenine (A), thymine (T), guanine (G) or cytosine (C).

C and T bases, which have just one ring, are called pyrimidines, while A and G bases, which have two rings, are called purines.

Left panel: structure of a DNA nucleotide. The deoxyribose sugar is attached to a phosphate group and to a nitrogenous base. The base may be any one of four possible options: cytosine (C), thymine (T), adenine (A), and guanine (G). The four bases have differences in their structure and functional groups. Cytosine and thymine are pyrimidines and have just one ring in their chemical structures. Adenine and guanine are purines and have two rings in their structures.

Right panel: a strand of linked DNA nucleotides. The sugars are connected by phosphodiester bonds. A phosphodiester bond consists of a phosphate group in which two of the oxygen atoms are bonded to other atoms - in this case, to carbon atoms of the neighboring deoxyribose sugars. The DNA strand consists of alternating phosphate groups and deoxyribose sugars (sugar-phosphate backbone), with the nitrogenous bases sticking out from the deoxyribose sugars.

DNA nucleotides assemble in chains linked by covalent bonds, which form between the deoxyribose sugar of one nucleotide and the phosphate group of the next. This arrangement makes an alternating chain of deoxyribose sugar and phosphate groups in the DNA polymer, a structure known as the sugar-phosphate backbone

Chargaff's rules

One other key piece of information related to the structure of DNA came from Austrian biochemist Erwin Chargaff. Chargaff analyzed the DNA of different species, determining its composition of A, T, C, and G bases. He made several key observations:

A, T, C, and G were not found in equal quantities (as some models at the time would have predicted)

The amounts of the bases varied among species, but not between individuals of the same species

The amount of A always equalled the amount of T, and the amount of C always equalled the amount of G (A = T and G = C)

These findings, called Chargaff's rules, turned out to be crucial to Watson and Crick's model of the DNA double helix.

Watson, Crick, and Rosalind Franklin

In the early 1950s, American biologist James Watson and British physicist Francis Crick came up with their famous model of the DNA double helix. They were the first to cross the finish line in this scientific "race," with others such as Linus Pauling (who discovered protein secondary structure) also trying to find the correct model.

Rather than carrying out new experiments in the lab, Watson and Crick mostly collected and analyzed existing pieces of data, putting them together in new and insightful ways2^22.
Some of their most crucial clues to DNA's structure came from Rosalind Franklin, a chemist working in the lab of physicist Maurice Wilkins.

Franklin was an expert in a powerful technique for determining the structure of molecules, known as X-ray crystallography. When the crystallized form of a molecule such as DNA is exposed to X-rays, some of the rays are deflected by the atoms in the crystal, forming a diffraction pattern that gives clues about the molecule's structure.

X-ray diffraction image of DNA. The diffraction pattern has an X shape representative of the two-stranded, helical structure of DNA.

Franklin’s crystallography gave Watson and Crick important clues to the structure of DNA. Some of these came from the famous “image 51,” a remarkably clear and striking X-ray diffraction image of DNA produced by Franklin and her graduate student. (A modern example of the diffraction pattern produced by DNA is shown above.) To Watson, the X-shaped diffraction pattern of Franklin's image immediately suggested a helical, two-stranded structure for DNA3^33.

Watson and Crick got additional information from an unpublished report by Franklin, which discussed the dimensions of the helix and the orientations of the two strands, details that proved crucial to their model3,4,5^{3,4,5}3,4,5. Franklin's report also included her conclusion that the nitrogenous bases were hidden on the inside of the DNA molecule6^{6}6.

Franklin's X-ray diffraction image and unpublished report were shown to Watson and Crick without Franklin's permission or knowledge. Interestingly, Franklin had shared most of the data contained in the report at an earlier, public presentation, one which Watson himself attended. Because Watson wasn't very familiar with chemistry and didn't take notes, however, he didn't remember the data correctly3,7^{3,7}3,7.

Watson and Crick did not steal Franklin's data per se, in that neither the diffraction image nor the report was confidential3^33. Nonetheless, they obtained and used her results in ways that showed a lack of transparency, professionalism, and respect. Watson and Crick did not ask Franklin for permission to interpret and use her data, nor did they acknowledge the extent of her contributions to their model (either when they published their work, or, nine years later, when they received the Nobel Prize)3,4,8^{3,4,8}3,4,8. Indeed, during her lifetime, Franklin probably never knew how extensively Watson and Crick had relied on her data in building their model3^33.

To learn more about the controversy surrounding Watson and Crick's professional relationship with Franklin, please see the sources cited in this portion of the article. (The references section at the end of the article contains direct links.)

Watson and Crick brought together data from a number of researchers (including Franklin, Wilkins, Chargaff, and others) to assemble their celebrated model of the 3D structure of DNA. In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine. Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously.

Watson and Crick's model of DNA

The structure of DNA, as represented in Watson and Crick's model, is a double-stranded, antiparallel, right-handed helix. The sugar-phosphate backbones of the DNA strands make up the outside of the helix, while the nitrogenous bases are found on the inside and form hydrogen-bonded pairs that hold the DNA strands together.

In the model below, the orange and red atoms mark the phosphates of the sugar-phosphate backbones, while the blue atoms on the interior of the helix belong to the nitrogenous bases.

Antiparallel orientation

Double-stranded DNA is an antiparallel molecule, meaning that it's composed of two strands that run alongside each other but point in opposite directions. In a double-stranded DNA molecule, the 5' end (phosphate-bearing end) of one strand aligns with the 3' end (hydroxyl-bearing end) of its partner, and vice versa.

The carbon atoms of the deoxyribose sugar in DNA nucleotides are labeled with numbers accompanied by prime marks. Prime marks look similar to apostrophes (e.g., 3').

The purpose of the prime marks is to distinguish the carbon atoms of the sugar from the ring atoms of the nitrogenous base. Carbon and nitrogen atoms in the rings of the nitrogenous bases are also given numbers, but these numbers don't have prime marks.

You can see the numbers assigned to ring carbons and nitrogens of the nitrogenous bases in the diagram below. The two-ring purines and one-ring pyrimidines have different numbering schemes, thanks to their different numbers of carbon atoms.

Structure of a DNA nucleotide, showing the numbering of the sugar carbons as well as the numbering of ring carbon and nitrogen atoms in the four potential nitrogenous bases (as well as uracil, a base found in RNA but not DNA). The nitrogenous bases are labeled with plain numbers, while the deoxyribose sugar is labeled with numbers accompanied by prime marks.

Left panel: illustration of the antiparallel structure of DNA. A short segment of DNA double helix is shown, composed of two DNA strands held together by hydrogen bonds between the bases. The strand on the left has a phosphate group exposed at its top (5' end) and a hydroxyl group exposed at its bottom (3' end). The strand on the right has the opposite orientation, with a phosphate group exposed at its bottom (5' end) and a hydroxyl exposed at its top (3' end). The 5' end of one strand thus ends up next to the 3' end of the other, and vice versa.

Right panel: structure of a nucleotide, illustrating the 5' phosphate group and 3' hydroxyl group. These groups get their names from their positions on the deoxyribose sugar's ring. The ring carbons of the sugar are labeled from 1' (the carbon bearing the nitrogenous base) to 5' (the carbon bearing the phosphate group). The 3' carbon in the middle bears the hydroxyl group.

Right-handed helix

In Watson and Crick's model, the two strands of DNA twist around each other to form a right-handed helix. All helices have a handedness, which is a property that describes how their grooves are oriented in space.

To understand what makes a helix right-handed, imagine wrapping your right hand around the DNA molecule shown in the figure, with your thumb pointing upwards. Now picture your fingers sliding along the outside of the spiral. Your hand should be moving with the spirals, upwards, in the direction your thumb is pointing. Because the right hand moves in the same direction as its thumb points as it slides along the spirals, the DNA double helix can be identified as right-handed9^99.

If you were to try the same thing with your left hand (thumb pointing up), your hand would instead slide downward, opposite to the direction in which its thumb is pointing.

Image of a DNA double helix, illustrating its right-handed structure. The major groove is a wider gap that spirals up the length of the molecule, while the minor groove is a smaller gap that runs in parallel to the major groove. The base pairs are found in the center of the helix, while the sugar-phosphate backbones run along the outside.

Not necessarily. Double-stranded DNA actually comes in three different forms, known as A-DNA, B-DNA, and Z-DNA. Although A-DNA and B-DNA are right-handed helices, Z-DNA is a left-handed helix10^{10}10.

The twisting of the DNA double helix and the geometry of the bases creates a wider gap (called the major groove) and a narrower gap (called the minor groove) that run along the length of the molecule, as shown in the figure above. These grooves are important binding sites for proteins that maintain DNA and regulate gene activity.

Base pairing

In Watson and Crick's model, the two strands of the DNA double helix are held together by hydrogen bonds between nitrogenous bases on opposite strands. Each pair of bases lies flat, forming a "rung" on the ladder of the DNA molecule.

Base pairs aren't made up of just any combination of bases. Instead, if there is an A found on one strand, it must be paired with a T on the other (and vice versa). Similarly, an G found on one strand must always have a C for a partner on the opposite strand. These A-T and G-C associations are known as complementary base pairs.

Diagram illustrating base pairing between A-T and G-C bases. A and T are found opposite to each other on the two strands of the helix, and their functional groups form two hydrogen bonds that hold the strands together. Similarly, G and C are found opposite to each other on the two strands, and their functional groups form three hydrogen bonds that hold the strands together.

Base pairing explains Chargaff's rules, that is, why the composition of A always equals that of T, and the composition of C equals that of G11^{11}11. Where there is an A in one strand, there must be a T in the other, and the same is true for G and C. Because a large purine (A or G) is always paired with a small pyrimidine (T or C), the diameter of the helix is uniform, coming in at about 222 nanometers.

Although Watson and Crick's original model proposed that there were two hydrogen bonds between the bases of each pair, we know today that G and C form an additional bond (such that A-T pairs form two hydrogen bonds total, while G-C pairs form three)12^{12}12.

The impact of the double helix

The structure of DNA unlocked the door to understanding many aspects of DNA's function, such as how it was copied and how the information it carried was used by the cell to make proteins.

As we'll see in upcoming articles and videos, Watson and Crick's model ushered in a new era of discovery in molecular biology. The model and the discoveries that it enabled form the foundations for much of today's cutting-edge research in biology and biomedicine.